'\" t
.TH samtools-bedcov 1 "14 July 2025" "samtools-1.22.1" "Bioinformatics tools"
.SH NAME
samtools bedcov \- reports coverage over regions in a supplied BED file
.\"
.\" Copyright (C) 2008-2011, 2013-2018, 2020, 2022, 2024 Genome Research Ltd.
.\" Portions copyright (C) 2010, 2011 Broad Institute.
.\"
.\" Author: Heng Li <lh3@sanger.ac.uk>
.\" Author: Joshua C. Randall <jcrandall@alum.mit.edu>
.\"
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.SH SYNOPSIS
.PP
samtools bedcov
.RI [ options ]
.IR region.bed " " in1.sam | in1.bam | in1.cram "[...]"

.SH DESCRIPTION
.PP

Reports the total read base count (i.e. the sum of per base read depths)
for each genomic region specified in the supplied BED file. The regions
are output as they appear in the BED file and are 0-based.
Columns 1-3 are chrom/start/end as per the input BED file, followed by N
columns of coverages (for N input BAMs), then (if given -d), N columns of
bases-at-depth-X, then (if given -c) N columns of read counts.

.SH OPTIONS
.TP
.BI "-Q,\ --min-MQ " INT
.RI "Only count reads with mapping quality greater than or equal to " INT
.TP
.BI "-g " FLAGS
By default, reads that have any of the flags UNMAP, SECONDARY, QCFAIL,
or DUP set are skipped. To include these reads back in the analysis, use
this option together with the desired flag or flag combination.
.I FLAGS
can be specified in hex by beginning with `0x' (i.e. /^0x[0-9A-F]+/),
in octal by beginning with `0' (i.e. /^0[0-7]+/), as a decimal number
not beginning with '0' or as a comma-separated list of flag names. [0]

For a list of flag names see
.IR samtools-flags (1).
.TP
.BI "-G " FLAGS
Discard any read that has any of the flags specified by
.I FLAGS
set.  FLAGS are specified as for the
.B "-g"
option. [UNMAP,SECONDARY,QCFAIL,DUP]
.TP
.B  -j
Do not include deletions (D) and ref skips (N) in bedcov computation.
.TP
.BI "-d " INT
Print an additional column, for each file, containing the number of bases having
a depth above and including the given threshold. If the option is not used, the
extra column is not displayed. The option value must be an integer >= 0.
.TP
.BI "--max-depth " INT
Specifies the maximum depth used for the mpileup algorithm.
If \fB-d\fR is used and is larger then this value will be used instead.
Defaults to 2 billion, but smaller values may be used when we do not
require an exact count in excessively deep regions and are interested
in maximizing speed of results.
.TP
.B -c
Print an additional column with the read count for this region.  This
will be +1 for every read covering the region, not just starting
within in.  The whole read filtering options \fB-Q\fR, \fB-g\fR and
\fB-G\fR options will also have an effect on this count, but \fB-d\fR
will not.
.TP
.B "-X"
If this option is set, it will allows user to specify customized index file
location(s) if the data folder does not contain any index file. Example usage:
samtools bedcov [options] -X <in.bed> </data_folder/in1.bam> [...]
</index_folder/index1.bai> [...]
.TP
.B "-H"
.R When a header starting in "#chrom" is available in the input bed file, it is
copied to the output. When it is not available, a header is created with field
names matching the fields listed in the GA4GH BED specification.
The \fB-c\fR and \fB-d\fR options can add further per-file columns named
.IR in1.sam "_count and " in1.sam "_depth along with " in1.sam "_count."

.SH AUTHOR
.PP
Written by Heng Li from the Sanger Institute.

.SH SEE ALSO
.IR samtools (1)
.PP
Samtools website: <http://www.htslib.org/>
